4LQR

Structure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J1APDB ENTRY 2J1A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820% PEG 10000, 100mM HEPES 50mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9436.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.766α = 90
b = 52.562β = 90
c = 70.169γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.15CCDADSC QUANTUM 2102009-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.98NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.585098.90.0425.420155
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.64910.0847.61833

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J1A1.5833.9620155102499.830.16260.16090.194RANDOM9.8579
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.42-0.110.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.04
r_dihedral_angle_4_deg16.052
r_dihedral_angle_3_deg12.037
r_dihedral_angle_1_deg7.194
r_angle_refined_deg2.248
r_chiral_restr0.178
r_bond_refined_d0.024
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing